Nextflow workflow report

[romantic_nightingale] (resumed run)

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 255.

The full error message was:

Error executing process > 'callVariants (8)'

Caused by:
  Process `callVariants (8)` terminated with an error exit status (255)

Command executed:

  echo "Starting BCFTools from within the container for STAT1_STAT1_HUMAN.H11MO.0.A on dataset JD32HPP..."
  
  bcftools mpileup -Ou -f "input-dir-cluster/refs/GRCh38_no_alt_GCA_000001405.15.fasta.gz" -T "STAT1_STAT1_HUMAN.H11MO.0.A_TOBIAS_TF_binding_sites-sorted.bed" -b "JD32HPP.bamlist.txt" --annotate FORMAT/AD,FORMAT/DP | bcftools call -Ou -mv | bcftools filter -i'QUAL>10' | bcftools +fill-tags - -- -t AF,VAF > "STAT1_STAT1_HUMAN.H11MO.0.A_qualgt10.var.flt.VAF.allTFBS_JD32HPP.vcf"

Command exit status:
  255

Command output:
  Starting BCFTools from within the container for STAT1_STAT1_HUMAN.H11MO.0.A on dataset JD32HPP...

Command error:
  [E::fai_build3_core] Failed to open the file input-dir-cluster/refs/GRCh38_no_alt_GCA_000001405.15.fasta.gz : No such file or directory
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type

Work dir:
  /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/a1/f7d6a1945c591e28cd713d1afb137c

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Run times
28-Feb-2024 11:11:50 - 28-Feb-2024 11:12:02 (duration: 11.9s)
  0 succeeded  
  1366 cached  
  0 ignored  
  1 failed  
Nextflow command
nextflow run -resume main.nf --run_mode subset --dataset_id_list input-dir-cluster/manifests/dataset-manifest-heme-cancers.txt --genome_fasta input-dir-cluster/refs/GRCh38_no_alt_GCA_000001405.15.fasta.gz --output_dir output-dir-cluster -c nextflow_cluster.config -with-dag workflow-reports/dag-20240228-11.11.html -with-report workflow-reports/report-20240228-11.11.html -with-timeline workflow-reports/timeline-20240228-11.11.html
CPU-Hours
1.1 (99.9% cached, 0.1% failed)
Launch directory
/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf
Work directory
/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work
Project directory
/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf
Script name
main.nf
Script ID
4af21cf2ab88a8442835b8986f4f9a49
Workflow session
140920df-0168-40f6-86d5-6f6c04264f45
Workflow profile
standard
Workflow container
/home/users/ntu/suffiazi/apps/sifs/bcftools-py.sif
Container engine
singularity
Nextflow version
version 23.10.1, build 5891 (12-01-2024 22:01 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Memory

Job Duration

I/O

Tasks

This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.

(tasks table omitted because the dataset is too big)